Merge branch 'main' into setup-emscripten-ci

Author: agriyakhetarpal

.flake8

@@ -1,4 +1,4 @@
-name: Linux CI
+name: Tests
 
 on: [push, pull_request]
 
@@ -8,11 +8,13 @@ concurrency:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.platform }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
+        # macos-12 is an intel runner, macos-14 is a arm64 runner
+        platform: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
     steps:
       - name: Checkout source
@@ -21,9 +23,10 @@ jobs:
           submodules: recursive
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v3.0.1
+        uses: conda-incubator/setup-miniconda@v3.1.0
         with:
             channels: conda-forge
+            miniforge-version: latest
             python-version: ${{ matrix.python-version }}
 
       - name: Show info about `base` environment
@@ -40,6 +43,13 @@ jobs:
           c-compiler cxx-compiler
           python=${{matrix.python-version}} wheel pip
 
+      - name: Install clang
+        shell: "bash -l {0}"
+        if: matrix.platform == 'macos-13'
+        run: |
+          conda activate env
+          conda install -y 'clang>=12.0.1,<17'
+
       - name: Show info about `env` environment
         shell: "bash -l {0}"
         run: |
@@ -50,31 +60,38 @@ jobs:
         run: |
           conda activate env
           export DISABLE_NUMCODECS_AVX2=""
-          python -m pip install -v -e .[test,test_extras,msgpack,zfpy,pcodec]
+          # TODO: put back zfpy import when it supports numpy 2.0
+          python -m pip install -v -e .[test,test_extras,msgpack,crc32c]
 
-      - name: List installed packages
+      - name: Install pcodec
+        if: matrix.python-version != '3.13'
+        shell: "bash -l {0}"
+        run: |
+            conda activate env
+            python -m pip install -v ".[pcodec]"
+
+
+      # This is used to test with zfpy, which does not yet support numpy 2.0
+      - name: Install older numpy and zfpy
+        if: matrix.python-version == '3.11'
         shell: "bash -l {0}"
         run: |
           conda activate env
-          python -m pip list
+          python -m pip install "zfpy>=1" "numpy<2"
 
-      - name: Flake8
+      - name: List installed packages
         shell: "bash -l {0}"
         run: |
           conda activate env
-          flake8
+          python -m pip list
 
       - name: Run tests
         shell: "bash -l {0}"
         run: |
           conda activate env
           pytest -v
 
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
-          #token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-            #files: ./coverage1.xml,./coverage2.xml # optional
-            #flags: unittests # optional
-            #name: codecov-umbrella # optional
-            #fail_ci_if_error: true # optional (default = false)
-          verbose: true # optional (default = false)
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true

.github/workflows/ci-osx.yaml

@@ -36,7 +36,7 @@ jobs:
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           languages: python
           # languages: python, cpp
@@ -45,7 +45,7 @@ jobs:
       # Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below).
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -59,4 +59,4 @@ jobs:
       #     make release
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3

.github/workflows/ci-windows.yaml

@@ -13,24 +13,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        # macos-13 is an intel runner, macos-14 is a arm64 runner
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
     env:
       CIBW_TEST_COMMAND: python -c "import numcodecs"
-      CIBW_SKIP: "pp* cp36-* *-musllinux_* *win32 *_i686 *_s390x"
-      CIBW_ARCHS_MACOS: 'x86_64 arm64'
-      CIBW_TEST_SKIP: '*-macosx_arm64'
+      CIBW_BUILD: "cp311-* cp312-* cp313-*"
+      CIBW_SKIP: "pp* *-musllinux_* *win32 *_i686 *_s390x"
       # note: CIBW_ENVIRONMENT is now set in pyproject.toml
-      
+
     steps:
       - uses: actions/checkout@v4
         with:
           submodules: true
 
-      - uses: pypa/cibuildwheel@v2.16.5
+      - uses: pypa/cibuildwheel@v2.21.3
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-${{ matrix.os }}
           path: ./wheelhouse
 
   build_sdist:
@@ -44,30 +44,32 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: "3.11"
 
       - name: Build sdist
         run: pipx run build --sdist
 
       - name: test install
         run: pip install dist/numcodecs*.tar.gz
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: sdist
           path: dist/*.tar.gz
 
   test_dist_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          name: sdist
           path: dist
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: wheels
+          pattern: wheels-*
           path: dist
+          merge-multiple: true
 
       - name: test
         run: |
@@ -79,14 +81,15 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          name: sdist
           path: dist
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: wheels
+          pattern: wheels-*
           path: dist
+          merge-multiple: true
 
       - uses: pypa/gh-action-pypi-publish@master
         with: